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- PDB-9jea: cryo-EM structure of M1 muscarinic acetylcholine receptor in comp... -

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Basic information

Entry
Database: PDB / ID: 9jea
Titlecryo-EM structure of M1 muscarinic acetylcholine receptor in complex with atropine
ComponentsMuscarinic acetylcholine receptor M1,de novo design protein
KeywordsMEMBRANE PROTEIN / GPCR / inactive-state / de novo protein
Function / homology
Function and homology information


saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport / neuromuscular synaptic transmission ...saliva secretion / regulation of glial cell proliferation / positive regulation of monoatomic ion transport / Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of intracellular protein transport / neuromuscular synaptic transmission / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / regulation of locomotion / regulation of postsynaptic membrane potential / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / postsynaptic modulation of chemical synaptic transmission / axon terminus / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / G protein-coupled acetylcholine receptor signaling pathway / nervous system development / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / synapse / dendrite / glutamatergic synapse / signal transduction / membrane / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M1 / Muscarinic acetylcholine receptor family / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
: / Muscarinic acetylcholine receptor M1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao, K. / Zhang, X. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81974236 China
CitationJournal: To Be Published
Title: cryo-EM structure of M1 muscarinic acetylcholine receptor in complex with atropine
Authors: Gao, K. / Zhang, X.
History
DepositionSep 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muscarinic acetylcholine receptor M1,de novo design protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1252
Polymers51,8351
Non-polymers2891
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Muscarinic acetylcholine receptor M1,de novo design protein


Mass: 51835.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11229
#2: Chemical ChemComp-A1EBT / [(1R,5S)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-oxidanyl-2-phenyl-propanoate / Atropine sulfate


Mass: 289.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: M1 muscarinic acetylcholine receptor/de novo design fusion protein
Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121129 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032801
ELECTRON MICROSCOPYf_angle_d0.5563833
ELECTRON MICROSCOPYf_dihedral_angle_d4.703405
ELECTRON MICROSCOPYf_chiral_restr0.037482
ELECTRON MICROSCOPYf_plane_restr0.004459

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